In lgatto/rauthoring: An introduction to authoring literate programming documents.

ReporingTools and knitr

Introduction

It is possible to include ReportingTools elements into knitr R markdown documents. Compiling such documents must be done with knitr::knit2html (instead of rmarkdown::render).

A table

nomsg <- capture.output(library("rauthoring"))
library("DESeq2")
data(res)
library("ReportingTools")
library("XML")

The following code chunk, with argument results='asis' will produce the dynamic table below. Note that we need to specify the final vignette destination directory (instDoc) for the JavaScript code to be effectively inserted in the vignette. If it were not for a vignette, the reportDirectory would be the directory containing the report file.

library("rauthoring")
data(res)
## must not be an instance of class DESeqResults
res <- data.frame(res[1:100, ])
library("ReportingTools")
library("XML")
instDoc <- file.path("..", "inst", "doc")
htmlRep <- HTMLReport(shortName = "knitrReport",
                      handlers = knitrHandlers,
                      reportDirectory = instDoc)
htmlRep[["res"]] <- res

library("rauthoring")
data(res)
res <- data.frame(res[1:100, ])
library("ReportingTools")
library("XML")
instDoc <- file.path("..", "inst", "doc")
htmlRep <- HTMLReport(shortName = "knitrReport",
                      handlers = knitrHandlers,
                      reportDirectory = instDoc)
htmlRep[["res"]] <- res